Semantic Reasoning Assembler and Mapper (SeMRA)

The Semantic Mapping Reasoner and Assembler (SeMRA; https://github.com/biopragmatics/semra) is an open source Python package that provides:

  1. An object model for semantic mappings (based on SSSOM)
  2. Functionality for assembling and reasoning over semantic mappings at scale
  3. A provenance model for automatically generated mappings
  4. A confidence model granular at the curator-level, mapping set-level, and community feedback-level

Artifacts

SeMRA was used to assemble a large-scale database of raw semantic mappings from hundreds of ontologies and databases in SSSOM: https://doi.org/10.5281/zenodo.11082038. This is periodically refreshed and can be rebuilt locally with semra build.

Domain-specific mapping assemblies listed here

Training Material

Publications

  • https://doi.org/10.1093/bioinformatics/btaf542